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legendplextm data analysis software suite  (Qognit Inc)

 
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    Qognit Inc legendplextm data analysis software suite
    Legendplextm Data Analysis Software Suite, supplied by Qognit Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/legendplextm+data+analysis+software+suite/analysis+based+cloud+data+legendplex+software/pm42156885-368-7-6
    Average 86 stars, based on 1 article reviews
    legendplextm data analysis software suite - by Bioz Stars, 2026-10
    86/100 stars

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    Related Articles

    Software:

    Article Title: Mitochondrial DNA variants and microbiota: An experimental strategy to identify novel therapeutic potential in chronic inflammatory diseases.
    Article Snippet: A LEGENDplexTM Mouse Inflammation Panel (13-plex) with a V-bottom Panel (Biolegend) was used to determine cytokine levels in the mouse serum samples. .. The FCS files were analysed using the LEGENDplexTM Data Analysis Software Suite (https://legendplex.qognit.com/user/login?next=home). .. GraphPad Prism v10 (GraphPad Software, Boston MA, USA) was used for statistical analyses (except the shotgun metagenomics sequencing data analysis).

    Article Title: Regulatory T Cell Phenotype Related to Cytokine Expression Patterns in Post-COVID-19 Pulmonary Fibrosis and Idiopathic Pulmonary Fibrosis.
    Article Snippet: Reactions were run in duplicate using a BD FACSLyric flow cytometer (BD‐Biosciences San Jose, CA, USA). .. Data analysis was done using the LEGENDplexTM Data Analysis Software Suite (QOGNIT). ..

    Article Title: Circumventing pyroptosis via hyperactivation shapes superior immune responses of human type 2 dendritic cells compared to type 3 dendritic cells.
    Article Snippet: .. Cytokine concentrations for IL-1β, IFN-α2, IFNγ, TNF-α, MCP-1, IL-6, IL-8, IL-10, IL-12p70, IL-17A, IL-18, IL-23, and IL-33 were then determined using the LEGENDplexTM Data Analysis Software Suite (Qognit). ..

    Article Title: Increased Herpesvirus Entry Mediator Expression on Circulating Monocytes and Subsets Predicts Poor Outcomes in Pancreatic Ductal Adenocarcinoma Patients.
    Article Snippet: .. Data acquisition was performed on flow cytometer and analyzed with the LEGENDPlexTM Data Analysis Software Suite (https://legendplex.qognit.com/workflow/171050 (accessed on 17 March 2025), Biolegend, San Diego, CA, USA). .. Data were stored on a laboratory computer and analyzed using GraphPad Prism (Version 9.5.1 (733) for Windows, GraphPad Software, Boston, MA, USA).

    Article Title: The MYB-related transcription factor MYPOP acts as a selective regulator of cancer cell growth.
    Article Snippet: Cytofluorometric analyses were performed with a flow cytometer FC500 and CXP analysis software (Beckman Coulter, USA). .. Data analysis was performed with the QOGNIT LEGENDplexTM Data Analysis Software Suite (version 2023- 02-15). .. The protein concentration of IL-24 at time points between 6 h and 54 h post mRNA transfection was quantified using the Human IL-24 DuoSet ELISA Kit (Bio-Techne, USA).

    Article Title: Bordetella spp. block eosinophil recruitment to suppress the generation of early mucosal protection.
    Article Snippet: Cat#130-095-927 MojoSortTM Mouse CD3+ T cell Isolation Kit BioLegend Cat#480024 DynabeadsTM Mouse T-Activator CD3/CD28 T cell Expansion and Activation Beads Gibco Cat #11456D NEBNext Library Quant Kit for Illumina New England Biolabs Cat# E7630L Stranded mRNA Prep Ligation kit Illumina Cat# 20040532 PureLink DNase Set Invitrogen Cat #12185010 Deposited data FASTQ files EMBL-EBI (https://www.ebi. ac.uk/biostudies/arrayexpress/ studies/E-MTAB-13332); LSU Health Sciences Center at Shreveport BioStudies: E-MTAB-13332 Mus musculus reference genome version GRCm39 Genome Reference Consortium (GRC) GenBank: GCA_000001635.9 Mus musculus gene transfer format (.gtf) annotated version GRCm39.105: GCA_000001635.9 NCBI RefSeq RefSeq: GCF_000001635.27-RS_2023_04 Experimental models: Cell lines Murine bone marrow-derived eosinophils Mai et al., 202174 PMID: 33486726 Experimental models: Organisms/strains Mouse: BALB/cJ Jackson Laboratories Cat# 000651; RRID: IMSR_JAX:000651 Mouse: DdblGATA: B6.129S1(C)-Gata1tm6Sho/LvtzJ Jackson Laboratories Cat# 033551; RRID: IMSR_JAX:033551 Mouse: C57BL/6J Jackson Laboratories Cat# 000664; RRID: IMSR_JAX:000664 Mouse: EPX/MBP / : MBP-1 / /EPX / Donation from Dr Jacobsen La Joya PMID: 28515227 Oligonucleotides b-Actin Fw IDT (Integrated DNA Technologies) PMID: 31889098 b-Actin Rv IDT (Integrated DNA Technologies) PMID: 31889098 Il-17 Fw IDT (Integrated DNA Technologies) PMID: 17918201 IL-17 Rv IDT (Integrated DNA Technologies) PMID: 17918201 IFNg Fw IDT (Integrated DNA Technologies) PMID: 23133493 IFNg Rv IDT (Integrated DNA Technologies) PMID: 23133493 CCL-19 F IDT (Integrated DNA Technologies) PMID: 19651862 CCL-19 Rv IDT (Integrated DNA Technologies) PMID: 19651862 (Continued on next page) Cell Reports 42, 113294, November 28, 2023 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER MadCam-1-Fw IDT (Integrated DNA Technologies) PMID: 31526758 MadCam-1-Rv IDT (Integrated DNA Technologies) PMID: 31526758 Software and algorithms LegendPlexTM Data Analysis Software Suite Qognit legendplex.qognit.com Keyence Image Analysis Software (version 1.1.2) Keyence Corporation America Cat# BZ-H4A, BZ-H4M, BZ-H4CM, BZ-H4R qRT-PCR fold-change mRNA expression The Ultimate qPCR Experiment: Producing Publication Quality, Reproducible Data the First Time: Trends in Biotechnology (cell.com) PMID: 30654913 Illumina NovaSeq Control Software v1.7.5; RTA v3 https://support.illumina.com/downloads/ novaseq-control-software-v1-7-5.html V 1.7.5; RTA v3 Trimmomatic adaptor (version 0.38) https://github.com/usadellab/ Trimmomatic/tree/main V 0.38 DESeq2 R package (version 1.34.0) https://doi.org/10.18129/B9.bioc.DESeq2 V 1.34.0 Cluster profiler package (version 4.2.2) https://doi.org/10.18129/ B9.bioc.clusterProfiler V 4.2.2 ashr’ shrunkage package https://github.com/stephens999/ashr N/A RSEM software (version 1.3.1) https://deweylab.github.io/RSEM/ V 1.3.1 STAR RNA-Seq Read Mapper (version 2.7) https://github.com/alexdobin/STAR; https://doi.org/10.1093/ bioinformatics/bts635 V 2.7 FlowJo (version 10.9) TreeStar, Ashland, OR V 10.9 GraphPad (version 10.0.2) https://www.graphpad.com V 10.0.2 Other Bulk cartridge CodePlex Secretome IsoPlexis Cat# CodePlex Inflammation-L Chip 2, CODEPLEX-@L-10-2 All-in-One Fluorescence Microscope Keyence Cat# BZ-X810 CFX96 Touch Real-Time PCR Bio-Rad Cat# CFX96 Touch Real-Time PCR Detection System NovaSeq 6000 Illumina Model: Illumina NovaSeq 6000 BaseSpace Sequence Hub Illumina https://www.illumina.com/products/ by-type/informatics-products/ basespace-sequence-hub.html NovoCyte Quanteon Flow Cytometer Agilent Cat#64-1-1812-1046-4 GentleMACS Octo Dissociator with Heaters Miltenyi Biotech Cat# 130-096-427 NanoDrop One-C NanoDrop Serial #A241601534 Countess 3 Automated Cell Counter Invitrogen Cat #AMQAX2000 Bead Mill Homogenizer 120V (25 mL-5mL) VWR-Avantor Cat#75840-022 DeNovix DS-11 FX Spectrophotometer Qubit https://www.denovix.com/products/ ds-11-fx-spectrophotometer-fluorometer/ 2 mL reinforced Bead Mill tubes VWR-Avantor Cat# 10158-556 0.4 mm glass beads VWR-Avantor Cat# 12621-154 1.4 mm ceramic beads VWR-Avantor Cat# 10158-552 Hard-Shell PCR Plates 96-well, thin wall Bio-Rad Cat# HSP9601 Microseal B seals Bio-Rad Cat# MSB1001 Miltenyi dissociation tubes Miltenyi Biotech Cat# 130-095-927 40mm filters Falcon Cat# 352340 Keyence BZ-X800E Keyence Corporation Cat# BZ-X800E 22 Cell Reports 42, 113294, November 28, 2023 ..

    Article Title: Tumor-mediated microbiota alteration impairs synaptic tagging/capture in the hippocampal CA1 area via IL-1β production.
    Article Snippet: The standard curve and the samples were measured using an BD FACSAriaTM Fusion Flow Cytometers (BD Bioscience, Franklin Lakes, NJ, USA). .. The results were analyzed with the LEGENDplexTM Data Analysis Software Suite from Qognit (https:// legendplex.qognit.com/user/login?next=home), which could differentiate specific beads for each analyte based on their size and fluorescence intensity, where 4000 events had to be acquired per analyte. ..

    Article Title: An effective approach to modulate mitochondrial function in murine primary macrophages by a mitochondria-targeted nanocapsule, MITO-Porter.
    Article Snippet: Macrophages play crucial roles in various pathological conditions as well as maintenance of homeostasis.. Many chronic inflammatory conditions, such as atherosclerosis, rheumatoid arthritis, and obesity, are known to involve the polarization of macrophages into a proinflammatory state.. Therefore, controlling the function of macrophages is a potential strategy to intervene in such pathological conditions.

    Flow Cytometry:

    Article Title: Increased Herpesvirus Entry Mediator Expression on Circulating Monocytes and Subsets Predicts Poor Outcomes in Pancreatic Ductal Adenocarcinoma Patients.
    Article Snippet: .. Data acquisition was performed on flow cytometer and analyzed with the LEGENDPlexTM Data Analysis Software Suite (https://legendplex.qognit.com/workflow/171050 (accessed on 17 March 2025), Biolegend, San Diego, CA, USA). .. Data were stored on a laboratory computer and analyzed using GraphPad Prism (Version 9.5.1 (733) for Windows, GraphPad Software, Boston, MA, USA).

    Article Title: Bordetella spp. block eosinophil recruitment to suppress the generation of early mucosal protection.
    Article Snippet: Cat#130-095-927 MojoSortTM Mouse CD3+ T cell Isolation Kit BioLegend Cat#480024 DynabeadsTM Mouse T-Activator CD3/CD28 T cell Expansion and Activation Beads Gibco Cat #11456D NEBNext Library Quant Kit for Illumina New England Biolabs Cat# E7630L Stranded mRNA Prep Ligation kit Illumina Cat# 20040532 PureLink DNase Set Invitrogen Cat #12185010 Deposited data FASTQ files EMBL-EBI (https://www.ebi. ac.uk/biostudies/arrayexpress/ studies/E-MTAB-13332); LSU Health Sciences Center at Shreveport BioStudies: E-MTAB-13332 Mus musculus reference genome version GRCm39 Genome Reference Consortium (GRC) GenBank: GCA_000001635.9 Mus musculus gene transfer format (.gtf) annotated version GRCm39.105: GCA_000001635.9 NCBI RefSeq RefSeq: GCF_000001635.27-RS_2023_04 Experimental models: Cell lines Murine bone marrow-derived eosinophils Mai et al., 202174 PMID: 33486726 Experimental models: Organisms/strains Mouse: BALB/cJ Jackson Laboratories Cat# 000651; RRID: IMSR_JAX:000651 Mouse: DdblGATA: B6.129S1(C)-Gata1tm6Sho/LvtzJ Jackson Laboratories Cat# 033551; RRID: IMSR_JAX:033551 Mouse: C57BL/6J Jackson Laboratories Cat# 000664; RRID: IMSR_JAX:000664 Mouse: EPX/MBP / : MBP-1 / /EPX / Donation from Dr Jacobsen La Joya PMID: 28515227 Oligonucleotides b-Actin Fw IDT (Integrated DNA Technologies) PMID: 31889098 b-Actin Rv IDT (Integrated DNA Technologies) PMID: 31889098 Il-17 Fw IDT (Integrated DNA Technologies) PMID: 17918201 IL-17 Rv IDT (Integrated DNA Technologies) PMID: 17918201 IFNg Fw IDT (Integrated DNA Technologies) PMID: 23133493 IFNg Rv IDT (Integrated DNA Technologies) PMID: 23133493 CCL-19 F IDT (Integrated DNA Technologies) PMID: 19651862 CCL-19 Rv IDT (Integrated DNA Technologies) PMID: 19651862 (Continued on next page) Cell Reports 42, 113294, November 28, 2023 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER MadCam-1-Fw IDT (Integrated DNA Technologies) PMID: 31526758 MadCam-1-Rv IDT (Integrated DNA Technologies) PMID: 31526758 Software and algorithms LegendPlexTM Data Analysis Software Suite Qognit legendplex.qognit.com Keyence Image Analysis Software (version 1.1.2) Keyence Corporation America Cat# BZ-H4A, BZ-H4M, BZ-H4CM, BZ-H4R qRT-PCR fold-change mRNA expression The Ultimate qPCR Experiment: Producing Publication Quality, Reproducible Data the First Time: Trends in Biotechnology (cell.com) PMID: 30654913 Illumina NovaSeq Control Software v1.7.5; RTA v3 https://support.illumina.com/downloads/ novaseq-control-software-v1-7-5.html V 1.7.5; RTA v3 Trimmomatic adaptor (version 0.38) https://github.com/usadellab/ Trimmomatic/tree/main V 0.38 DESeq2 R package (version 1.34.0) https://doi.org/10.18129/B9.bioc.DESeq2 V 1.34.0 Cluster profiler package (version 4.2.2) https://doi.org/10.18129/ B9.bioc.clusterProfiler V 4.2.2 ashr’ shrunkage package https://github.com/stephens999/ashr N/A RSEM software (version 1.3.1) https://deweylab.github.io/RSEM/ V 1.3.1 STAR RNA-Seq Read Mapper (version 2.7) https://github.com/alexdobin/STAR; https://doi.org/10.1093/ bioinformatics/bts635 V 2.7 FlowJo (version 10.9) TreeStar, Ashland, OR V 10.9 GraphPad (version 10.0.2) https://www.graphpad.com V 10.0.2 Other Bulk cartridge CodePlex Secretome IsoPlexis Cat# CodePlex Inflammation-L Chip 2, CODEPLEX-@L-10-2 All-in-One Fluorescence Microscope Keyence Cat# BZ-X810 CFX96 Touch Real-Time PCR Bio-Rad Cat# CFX96 Touch Real-Time PCR Detection System NovaSeq 6000 Illumina Model: Illumina NovaSeq 6000 BaseSpace Sequence Hub Illumina https://www.illumina.com/products/ by-type/informatics-products/ basespace-sequence-hub.html NovoCyte Quanteon Flow Cytometer Agilent Cat#64-1-1812-1046-4 GentleMACS Octo Dissociator with Heaters Miltenyi Biotech Cat# 130-096-427 NanoDrop One-C NanoDrop Serial #A241601534 Countess 3 Automated Cell Counter Invitrogen Cat #AMQAX2000 Bead Mill Homogenizer 120V (25 mL-5mL) VWR-Avantor Cat#75840-022 DeNovix DS-11 FX Spectrophotometer Qubit https://www.denovix.com/products/ ds-11-fx-spectrophotometer-fluorometer/ 2 mL reinforced Bead Mill tubes VWR-Avantor Cat# 10158-556 0.4 mm glass beads VWR-Avantor Cat# 12621-154 1.4 mm ceramic beads VWR-Avantor Cat# 10158-552 Hard-Shell PCR Plates 96-well, thin wall Bio-Rad Cat# HSP9601 Microseal B seals Bio-Rad Cat# MSB1001 Miltenyi dissociation tubes Miltenyi Biotech Cat# 130-095-927 40mm filters Falcon Cat# 352340 Keyence BZ-X800E Keyence Corporation Cat# BZ-X800E 22 Cell Reports 42, 113294, November 28, 2023 ..

    Quantitative RT-PCR:

    Article Title: Bordetella spp. block eosinophil recruitment to suppress the generation of early mucosal protection.
    Article Snippet: Cat#130-095-927 MojoSortTM Mouse CD3+ T cell Isolation Kit BioLegend Cat#480024 DynabeadsTM Mouse T-Activator CD3/CD28 T cell Expansion and Activation Beads Gibco Cat #11456D NEBNext Library Quant Kit for Illumina New England Biolabs Cat# E7630L Stranded mRNA Prep Ligation kit Illumina Cat# 20040532 PureLink DNase Set Invitrogen Cat #12185010 Deposited data FASTQ files EMBL-EBI (https://www.ebi. ac.uk/biostudies/arrayexpress/ studies/E-MTAB-13332); LSU Health Sciences Center at Shreveport BioStudies: E-MTAB-13332 Mus musculus reference genome version GRCm39 Genome Reference Consortium (GRC) GenBank: GCA_000001635.9 Mus musculus gene transfer format (.gtf) annotated version GRCm39.105: GCA_000001635.9 NCBI RefSeq RefSeq: GCF_000001635.27-RS_2023_04 Experimental models: Cell lines Murine bone marrow-derived eosinophils Mai et al., 202174 PMID: 33486726 Experimental models: Organisms/strains Mouse: BALB/cJ Jackson Laboratories Cat# 000651; RRID: IMSR_JAX:000651 Mouse: DdblGATA: B6.129S1(C)-Gata1tm6Sho/LvtzJ Jackson Laboratories Cat# 033551; RRID: IMSR_JAX:033551 Mouse: C57BL/6J Jackson Laboratories Cat# 000664; RRID: IMSR_JAX:000664 Mouse: EPX/MBP / : MBP-1 / /EPX / Donation from Dr Jacobsen La Joya PMID: 28515227 Oligonucleotides b-Actin Fw IDT (Integrated DNA Technologies) PMID: 31889098 b-Actin Rv IDT (Integrated DNA Technologies) PMID: 31889098 Il-17 Fw IDT (Integrated DNA Technologies) PMID: 17918201 IL-17 Rv IDT (Integrated DNA Technologies) PMID: 17918201 IFNg Fw IDT (Integrated DNA Technologies) PMID: 23133493 IFNg Rv IDT (Integrated DNA Technologies) PMID: 23133493 CCL-19 F IDT (Integrated DNA Technologies) PMID: 19651862 CCL-19 Rv IDT (Integrated DNA Technologies) PMID: 19651862 (Continued on next page) Cell Reports 42, 113294, November 28, 2023 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER MadCam-1-Fw IDT (Integrated DNA Technologies) PMID: 31526758 MadCam-1-Rv IDT (Integrated DNA Technologies) PMID: 31526758 Software and algorithms LegendPlexTM Data Analysis Software Suite Qognit legendplex.qognit.com Keyence Image Analysis Software (version 1.1.2) Keyence Corporation America Cat# BZ-H4A, BZ-H4M, BZ-H4CM, BZ-H4R qRT-PCR fold-change mRNA expression The Ultimate qPCR Experiment: Producing Publication Quality, Reproducible Data the First Time: Trends in Biotechnology (cell.com) PMID: 30654913 Illumina NovaSeq Control Software v1.7.5; RTA v3 https://support.illumina.com/downloads/ novaseq-control-software-v1-7-5.html V 1.7.5; RTA v3 Trimmomatic adaptor (version 0.38) https://github.com/usadellab/ Trimmomatic/tree/main V 0.38 DESeq2 R package (version 1.34.0) https://doi.org/10.18129/B9.bioc.DESeq2 V 1.34.0 Cluster profiler package (version 4.2.2) https://doi.org/10.18129/ B9.bioc.clusterProfiler V 4.2.2 ashr’ shrunkage package https://github.com/stephens999/ashr N/A RSEM software (version 1.3.1) https://deweylab.github.io/RSEM/ V 1.3.1 STAR RNA-Seq Read Mapper (version 2.7) https://github.com/alexdobin/STAR; https://doi.org/10.1093/ bioinformatics/bts635 V 2.7 FlowJo (version 10.9) TreeStar, Ashland, OR V 10.9 GraphPad (version 10.0.2) https://www.graphpad.com V 10.0.2 Other Bulk cartridge CodePlex Secretome IsoPlexis Cat# CodePlex Inflammation-L Chip 2, CODEPLEX-@L-10-2 All-in-One Fluorescence Microscope Keyence Cat# BZ-X810 CFX96 Touch Real-Time PCR Bio-Rad Cat# CFX96 Touch Real-Time PCR Detection System NovaSeq 6000 Illumina Model: Illumina NovaSeq 6000 BaseSpace Sequence Hub Illumina https://www.illumina.com/products/ by-type/informatics-products/ basespace-sequence-hub.html NovoCyte Quanteon Flow Cytometer Agilent Cat#64-1-1812-1046-4 GentleMACS Octo Dissociator with Heaters Miltenyi Biotech Cat# 130-096-427 NanoDrop One-C NanoDrop Serial #A241601534 Countess 3 Automated Cell Counter Invitrogen Cat #AMQAX2000 Bead Mill Homogenizer 120V (25 mL-5mL) VWR-Avantor Cat#75840-022 DeNovix DS-11 FX Spectrophotometer Qubit https://www.denovix.com/products/ ds-11-fx-spectrophotometer-fluorometer/ 2 mL reinforced Bead Mill tubes VWR-Avantor Cat# 10158-556 0.4 mm glass beads VWR-Avantor Cat# 12621-154 1.4 mm ceramic beads VWR-Avantor Cat# 10158-552 Hard-Shell PCR Plates 96-well, thin wall Bio-Rad Cat# HSP9601 Microseal B seals Bio-Rad Cat# MSB1001 Miltenyi dissociation tubes Miltenyi Biotech Cat# 130-095-927 40mm filters Falcon Cat# 352340 Keyence BZ-X800E Keyence Corporation Cat# BZ-X800E 22 Cell Reports 42, 113294, November 28, 2023 ..

    Expressing:

    Article Title: Bordetella spp. block eosinophil recruitment to suppress the generation of early mucosal protection.
    Article Snippet: Cat#130-095-927 MojoSortTM Mouse CD3+ T cell Isolation Kit BioLegend Cat#480024 DynabeadsTM Mouse T-Activator CD3/CD28 T cell Expansion and Activation Beads Gibco Cat #11456D NEBNext Library Quant Kit for Illumina New England Biolabs Cat# E7630L Stranded mRNA Prep Ligation kit Illumina Cat# 20040532 PureLink DNase Set Invitrogen Cat #12185010 Deposited data FASTQ files EMBL-EBI (https://www.ebi. ac.uk/biostudies/arrayexpress/ studies/E-MTAB-13332); LSU Health Sciences Center at Shreveport BioStudies: E-MTAB-13332 Mus musculus reference genome version GRCm39 Genome Reference Consortium (GRC) GenBank: GCA_000001635.9 Mus musculus gene transfer format (.gtf) annotated version GRCm39.105: GCA_000001635.9 NCBI RefSeq RefSeq: GCF_000001635.27-RS_2023_04 Experimental models: Cell lines Murine bone marrow-derived eosinophils Mai et al., 202174 PMID: 33486726 Experimental models: Organisms/strains Mouse: BALB/cJ Jackson Laboratories Cat# 000651; RRID: IMSR_JAX:000651 Mouse: DdblGATA: B6.129S1(C)-Gata1tm6Sho/LvtzJ Jackson Laboratories Cat# 033551; RRID: IMSR_JAX:033551 Mouse: C57BL/6J Jackson Laboratories Cat# 000664; RRID: IMSR_JAX:000664 Mouse: EPX/MBP / : MBP-1 / /EPX / Donation from Dr Jacobsen La Joya PMID: 28515227 Oligonucleotides b-Actin Fw IDT (Integrated DNA Technologies) PMID: 31889098 b-Actin Rv IDT (Integrated DNA Technologies) PMID: 31889098 Il-17 Fw IDT (Integrated DNA Technologies) PMID: 17918201 IL-17 Rv IDT (Integrated DNA Technologies) PMID: 17918201 IFNg Fw IDT (Integrated DNA Technologies) PMID: 23133493 IFNg Rv IDT (Integrated DNA Technologies) PMID: 23133493 CCL-19 F IDT (Integrated DNA Technologies) PMID: 19651862 CCL-19 Rv IDT (Integrated DNA Technologies) PMID: 19651862 (Continued on next page) Cell Reports 42, 113294, November 28, 2023 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER MadCam-1-Fw IDT (Integrated DNA Technologies) PMID: 31526758 MadCam-1-Rv IDT (Integrated DNA Technologies) PMID: 31526758 Software and algorithms LegendPlexTM Data Analysis Software Suite Qognit legendplex.qognit.com Keyence Image Analysis Software (version 1.1.2) Keyence Corporation America Cat# BZ-H4A, BZ-H4M, BZ-H4CM, BZ-H4R qRT-PCR fold-change mRNA expression The Ultimate qPCR Experiment: Producing Publication Quality, Reproducible Data the First Time: Trends in Biotechnology (cell.com) PMID: 30654913 Illumina NovaSeq Control Software v1.7.5; RTA v3 https://support.illumina.com/downloads/ novaseq-control-software-v1-7-5.html V 1.7.5; RTA v3 Trimmomatic adaptor (version 0.38) https://github.com/usadellab/ Trimmomatic/tree/main V 0.38 DESeq2 R package (version 1.34.0) https://doi.org/10.18129/B9.bioc.DESeq2 V 1.34.0 Cluster profiler package (version 4.2.2) https://doi.org/10.18129/ B9.bioc.clusterProfiler V 4.2.2 ashr’ shrunkage package https://github.com/stephens999/ashr N/A RSEM software (version 1.3.1) https://deweylab.github.io/RSEM/ V 1.3.1 STAR RNA-Seq Read Mapper (version 2.7) https://github.com/alexdobin/STAR; https://doi.org/10.1093/ bioinformatics/bts635 V 2.7 FlowJo (version 10.9) TreeStar, Ashland, OR V 10.9 GraphPad (version 10.0.2) https://www.graphpad.com V 10.0.2 Other Bulk cartridge CodePlex Secretome IsoPlexis Cat# CodePlex Inflammation-L Chip 2, CODEPLEX-@L-10-2 All-in-One Fluorescence Microscope Keyence Cat# BZ-X810 CFX96 Touch Real-Time PCR Bio-Rad Cat# CFX96 Touch Real-Time PCR Detection System NovaSeq 6000 Illumina Model: Illumina NovaSeq 6000 BaseSpace Sequence Hub Illumina https://www.illumina.com/products/ by-type/informatics-products/ basespace-sequence-hub.html NovoCyte Quanteon Flow Cytometer Agilent Cat#64-1-1812-1046-4 GentleMACS Octo Dissociator with Heaters Miltenyi Biotech Cat# 130-096-427 NanoDrop One-C NanoDrop Serial #A241601534 Countess 3 Automated Cell Counter Invitrogen Cat #AMQAX2000 Bead Mill Homogenizer 120V (25 mL-5mL) VWR-Avantor Cat#75840-022 DeNovix DS-11 FX Spectrophotometer Qubit https://www.denovix.com/products/ ds-11-fx-spectrophotometer-fluorometer/ 2 mL reinforced Bead Mill tubes VWR-Avantor Cat# 10158-556 0.4 mm glass beads VWR-Avantor Cat# 12621-154 1.4 mm ceramic beads VWR-Avantor Cat# 10158-552 Hard-Shell PCR Plates 96-well, thin wall Bio-Rad Cat# HSP9601 Microseal B seals Bio-Rad Cat# MSB1001 Miltenyi dissociation tubes Miltenyi Biotech Cat# 130-095-927 40mm filters Falcon Cat# 352340 Keyence BZ-X800E Keyence Corporation Cat# BZ-X800E 22 Cell Reports 42, 113294, November 28, 2023 ..

    Real-time Polymerase Chain Reaction:

    Article Title: Bordetella spp. block eosinophil recruitment to suppress the generation of early mucosal protection.
    Article Snippet: Cat#130-095-927 MojoSortTM Mouse CD3+ T cell Isolation Kit BioLegend Cat#480024 DynabeadsTM Mouse T-Activator CD3/CD28 T cell Expansion and Activation Beads Gibco Cat #11456D NEBNext Library Quant Kit for Illumina New England Biolabs Cat# E7630L Stranded mRNA Prep Ligation kit Illumina Cat# 20040532 PureLink DNase Set Invitrogen Cat #12185010 Deposited data FASTQ files EMBL-EBI (https://www.ebi. ac.uk/biostudies/arrayexpress/ studies/E-MTAB-13332); LSU Health Sciences Center at Shreveport BioStudies: E-MTAB-13332 Mus musculus reference genome version GRCm39 Genome Reference Consortium (GRC) GenBank: GCA_000001635.9 Mus musculus gene transfer format (.gtf) annotated version GRCm39.105: GCA_000001635.9 NCBI RefSeq RefSeq: GCF_000001635.27-RS_2023_04 Experimental models: Cell lines Murine bone marrow-derived eosinophils Mai et al., 202174 PMID: 33486726 Experimental models: Organisms/strains Mouse: BALB/cJ Jackson Laboratories Cat# 000651; RRID: IMSR_JAX:000651 Mouse: DdblGATA: B6.129S1(C)-Gata1tm6Sho/LvtzJ Jackson Laboratories Cat# 033551; RRID: IMSR_JAX:033551 Mouse: C57BL/6J Jackson Laboratories Cat# 000664; RRID: IMSR_JAX:000664 Mouse: EPX/MBP / : MBP-1 / /EPX / Donation from Dr Jacobsen La Joya PMID: 28515227 Oligonucleotides b-Actin Fw IDT (Integrated DNA Technologies) PMID: 31889098 b-Actin Rv IDT (Integrated DNA Technologies) PMID: 31889098 Il-17 Fw IDT (Integrated DNA Technologies) PMID: 17918201 IL-17 Rv IDT (Integrated DNA Technologies) PMID: 17918201 IFNg Fw IDT (Integrated DNA Technologies) PMID: 23133493 IFNg Rv IDT (Integrated DNA Technologies) PMID: 23133493 CCL-19 F IDT (Integrated DNA Technologies) PMID: 19651862 CCL-19 Rv IDT (Integrated DNA Technologies) PMID: 19651862 (Continued on next page) Cell Reports 42, 113294, November 28, 2023 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER MadCam-1-Fw IDT (Integrated DNA Technologies) PMID: 31526758 MadCam-1-Rv IDT (Integrated DNA Technologies) PMID: 31526758 Software and algorithms LegendPlexTM Data Analysis Software Suite Qognit legendplex.qognit.com Keyence Image Analysis Software (version 1.1.2) Keyence Corporation America Cat# BZ-H4A, BZ-H4M, BZ-H4CM, BZ-H4R qRT-PCR fold-change mRNA expression The Ultimate qPCR Experiment: Producing Publication Quality, Reproducible Data the First Time: Trends in Biotechnology (cell.com) PMID: 30654913 Illumina NovaSeq Control Software v1.7.5; RTA v3 https://support.illumina.com/downloads/ novaseq-control-software-v1-7-5.html V 1.7.5; RTA v3 Trimmomatic adaptor (version 0.38) https://github.com/usadellab/ Trimmomatic/tree/main V 0.38 DESeq2 R package (version 1.34.0) https://doi.org/10.18129/B9.bioc.DESeq2 V 1.34.0 Cluster profiler package (version 4.2.2) https://doi.org/10.18129/ B9.bioc.clusterProfiler V 4.2.2 ashr’ shrunkage package https://github.com/stephens999/ashr N/A RSEM software (version 1.3.1) https://deweylab.github.io/RSEM/ V 1.3.1 STAR RNA-Seq Read Mapper (version 2.7) https://github.com/alexdobin/STAR; https://doi.org/10.1093/ bioinformatics/bts635 V 2.7 FlowJo (version 10.9) TreeStar, Ashland, OR V 10.9 GraphPad (version 10.0.2) https://www.graphpad.com V 10.0.2 Other Bulk cartridge CodePlex Secretome IsoPlexis Cat# CodePlex Inflammation-L Chip 2, CODEPLEX-@L-10-2 All-in-One Fluorescence Microscope Keyence Cat# BZ-X810 CFX96 Touch Real-Time PCR Bio-Rad Cat# CFX96 Touch Real-Time PCR Detection System NovaSeq 6000 Illumina Model: Illumina NovaSeq 6000 BaseSpace Sequence Hub Illumina https://www.illumina.com/products/ by-type/informatics-products/ basespace-sequence-hub.html NovoCyte Quanteon Flow Cytometer Agilent Cat#64-1-1812-1046-4 GentleMACS Octo Dissociator with Heaters Miltenyi Biotech Cat# 130-096-427 NanoDrop One-C NanoDrop Serial #A241601534 Countess 3 Automated Cell Counter Invitrogen Cat #AMQAX2000 Bead Mill Homogenizer 120V (25 mL-5mL) VWR-Avantor Cat#75840-022 DeNovix DS-11 FX Spectrophotometer Qubit https://www.denovix.com/products/ ds-11-fx-spectrophotometer-fluorometer/ 2 mL reinforced Bead Mill tubes VWR-Avantor Cat# 10158-556 0.4 mm glass beads VWR-Avantor Cat# 12621-154 1.4 mm ceramic beads VWR-Avantor Cat# 10158-552 Hard-Shell PCR Plates 96-well, thin wall Bio-Rad Cat# HSP9601 Microseal B seals Bio-Rad Cat# MSB1001 Miltenyi dissociation tubes Miltenyi Biotech Cat# 130-095-927 40mm filters Falcon Cat# 352340 Keyence BZ-X800E Keyence Corporation Cat# BZ-X800E 22 Cell Reports 42, 113294, November 28, 2023 ..

    Control:

    Article Title: Bordetella spp. block eosinophil recruitment to suppress the generation of early mucosal protection.
    Article Snippet: Cat#130-095-927 MojoSortTM Mouse CD3+ T cell Isolation Kit BioLegend Cat#480024 DynabeadsTM Mouse T-Activator CD3/CD28 T cell Expansion and Activation Beads Gibco Cat #11456D NEBNext Library Quant Kit for Illumina New England Biolabs Cat# E7630L Stranded mRNA Prep Ligation kit Illumina Cat# 20040532 PureLink DNase Set Invitrogen Cat #12185010 Deposited data FASTQ files EMBL-EBI (https://www.ebi. ac.uk/biostudies/arrayexpress/ studies/E-MTAB-13332); LSU Health Sciences Center at Shreveport BioStudies: E-MTAB-13332 Mus musculus reference genome version GRCm39 Genome Reference Consortium (GRC) GenBank: GCA_000001635.9 Mus musculus gene transfer format (.gtf) annotated version GRCm39.105: GCA_000001635.9 NCBI RefSeq RefSeq: GCF_000001635.27-RS_2023_04 Experimental models: Cell lines Murine bone marrow-derived eosinophils Mai et al., 202174 PMID: 33486726 Experimental models: Organisms/strains Mouse: BALB/cJ Jackson Laboratories Cat# 000651; RRID: IMSR_JAX:000651 Mouse: DdblGATA: B6.129S1(C)-Gata1tm6Sho/LvtzJ Jackson Laboratories Cat# 033551; RRID: IMSR_JAX:033551 Mouse: C57BL/6J Jackson Laboratories Cat# 000664; RRID: IMSR_JAX:000664 Mouse: EPX/MBP / : MBP-1 / /EPX / Donation from Dr Jacobsen La Joya PMID: 28515227 Oligonucleotides b-Actin Fw IDT (Integrated DNA Technologies) PMID: 31889098 b-Actin Rv IDT (Integrated DNA Technologies) PMID: 31889098 Il-17 Fw IDT (Integrated DNA Technologies) PMID: 17918201 IL-17 Rv IDT (Integrated DNA Technologies) PMID: 17918201 IFNg Fw IDT (Integrated DNA Technologies) PMID: 23133493 IFNg Rv IDT (Integrated DNA Technologies) PMID: 23133493 CCL-19 F IDT (Integrated DNA Technologies) PMID: 19651862 CCL-19 Rv IDT (Integrated DNA Technologies) PMID: 19651862 (Continued on next page) Cell Reports 42, 113294, November 28, 2023 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER MadCam-1-Fw IDT (Integrated DNA Technologies) PMID: 31526758 MadCam-1-Rv IDT (Integrated DNA Technologies) PMID: 31526758 Software and algorithms LegendPlexTM Data Analysis Software Suite Qognit legendplex.qognit.com Keyence Image Analysis Software (version 1.1.2) Keyence Corporation America Cat# BZ-H4A, BZ-H4M, BZ-H4CM, BZ-H4R qRT-PCR fold-change mRNA expression The Ultimate qPCR Experiment: Producing Publication Quality, Reproducible Data the First Time: Trends in Biotechnology (cell.com) PMID: 30654913 Illumina NovaSeq Control Software v1.7.5; RTA v3 https://support.illumina.com/downloads/ novaseq-control-software-v1-7-5.html V 1.7.5; RTA v3 Trimmomatic adaptor (version 0.38) https://github.com/usadellab/ Trimmomatic/tree/main V 0.38 DESeq2 R package (version 1.34.0) https://doi.org/10.18129/B9.bioc.DESeq2 V 1.34.0 Cluster profiler package (version 4.2.2) https://doi.org/10.18129/ B9.bioc.clusterProfiler V 4.2.2 ashr’ shrunkage package https://github.com/stephens999/ashr N/A RSEM software (version 1.3.1) https://deweylab.github.io/RSEM/ V 1.3.1 STAR RNA-Seq Read Mapper (version 2.7) https://github.com/alexdobin/STAR; https://doi.org/10.1093/ bioinformatics/bts635 V 2.7 FlowJo (version 10.9) TreeStar, Ashland, OR V 10.9 GraphPad (version 10.0.2) https://www.graphpad.com V 10.0.2 Other Bulk cartridge CodePlex Secretome IsoPlexis Cat# CodePlex Inflammation-L Chip 2, CODEPLEX-@L-10-2 All-in-One Fluorescence Microscope Keyence Cat# BZ-X810 CFX96 Touch Real-Time PCR Bio-Rad Cat# CFX96 Touch Real-Time PCR Detection System NovaSeq 6000 Illumina Model: Illumina NovaSeq 6000 BaseSpace Sequence Hub Illumina https://www.illumina.com/products/ by-type/informatics-products/ basespace-sequence-hub.html NovoCyte Quanteon Flow Cytometer Agilent Cat#64-1-1812-1046-4 GentleMACS Octo Dissociator with Heaters Miltenyi Biotech Cat# 130-096-427 NanoDrop One-C NanoDrop Serial #A241601534 Countess 3 Automated Cell Counter Invitrogen Cat #AMQAX2000 Bead Mill Homogenizer 120V (25 mL-5mL) VWR-Avantor Cat#75840-022 DeNovix DS-11 FX Spectrophotometer Qubit https://www.denovix.com/products/ ds-11-fx-spectrophotometer-fluorometer/ 2 mL reinforced Bead Mill tubes VWR-Avantor Cat# 10158-556 0.4 mm glass beads VWR-Avantor Cat# 12621-154 1.4 mm ceramic beads VWR-Avantor Cat# 10158-552 Hard-Shell PCR Plates 96-well, thin wall Bio-Rad Cat# HSP9601 Microseal B seals Bio-Rad Cat# MSB1001 Miltenyi dissociation tubes Miltenyi Biotech Cat# 130-095-927 40mm filters Falcon Cat# 352340 Keyence BZ-X800E Keyence Corporation Cat# BZ-X800E 22 Cell Reports 42, 113294, November 28, 2023 ..

    Fluorescence:

    Article Title: Bordetella spp. block eosinophil recruitment to suppress the generation of early mucosal protection.
    Article Snippet: Cat#130-095-927 MojoSortTM Mouse CD3+ T cell Isolation Kit BioLegend Cat#480024 DynabeadsTM Mouse T-Activator CD3/CD28 T cell Expansion and Activation Beads Gibco Cat #11456D NEBNext Library Quant Kit for Illumina New England Biolabs Cat# E7630L Stranded mRNA Prep Ligation kit Illumina Cat# 20040532 PureLink DNase Set Invitrogen Cat #12185010 Deposited data FASTQ files EMBL-EBI (https://www.ebi. ac.uk/biostudies/arrayexpress/ studies/E-MTAB-13332); LSU Health Sciences Center at Shreveport BioStudies: E-MTAB-13332 Mus musculus reference genome version GRCm39 Genome Reference Consortium (GRC) GenBank: GCA_000001635.9 Mus musculus gene transfer format (.gtf) annotated version GRCm39.105: GCA_000001635.9 NCBI RefSeq RefSeq: GCF_000001635.27-RS_2023_04 Experimental models: Cell lines Murine bone marrow-derived eosinophils Mai et al., 202174 PMID: 33486726 Experimental models: Organisms/strains Mouse: BALB/cJ Jackson Laboratories Cat# 000651; RRID: IMSR_JAX:000651 Mouse: DdblGATA: B6.129S1(C)-Gata1tm6Sho/LvtzJ Jackson Laboratories Cat# 033551; RRID: IMSR_JAX:033551 Mouse: C57BL/6J Jackson Laboratories Cat# 000664; RRID: IMSR_JAX:000664 Mouse: EPX/MBP / : MBP-1 / /EPX / Donation from Dr Jacobsen La Joya PMID: 28515227 Oligonucleotides b-Actin Fw IDT (Integrated DNA Technologies) PMID: 31889098 b-Actin Rv IDT (Integrated DNA Technologies) PMID: 31889098 Il-17 Fw IDT (Integrated DNA Technologies) PMID: 17918201 IL-17 Rv IDT (Integrated DNA Technologies) PMID: 17918201 IFNg Fw IDT (Integrated DNA Technologies) PMID: 23133493 IFNg Rv IDT (Integrated DNA Technologies) PMID: 23133493 CCL-19 F IDT (Integrated DNA Technologies) PMID: 19651862 CCL-19 Rv IDT (Integrated DNA Technologies) PMID: 19651862 (Continued on next page) Cell Reports 42, 113294, November 28, 2023 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER MadCam-1-Fw IDT (Integrated DNA Technologies) PMID: 31526758 MadCam-1-Rv IDT (Integrated DNA Technologies) PMID: 31526758 Software and algorithms LegendPlexTM Data Analysis Software Suite Qognit legendplex.qognit.com Keyence Image Analysis Software (version 1.1.2) Keyence Corporation America Cat# BZ-H4A, BZ-H4M, BZ-H4CM, BZ-H4R qRT-PCR fold-change mRNA expression The Ultimate qPCR Experiment: Producing Publication Quality, Reproducible Data the First Time: Trends in Biotechnology (cell.com) PMID: 30654913 Illumina NovaSeq Control Software v1.7.5; RTA v3 https://support.illumina.com/downloads/ novaseq-control-software-v1-7-5.html V 1.7.5; RTA v3 Trimmomatic adaptor (version 0.38) https://github.com/usadellab/ Trimmomatic/tree/main V 0.38 DESeq2 R package (version 1.34.0) https://doi.org/10.18129/B9.bioc.DESeq2 V 1.34.0 Cluster profiler package (version 4.2.2) https://doi.org/10.18129/ B9.bioc.clusterProfiler V 4.2.2 ashr’ shrunkage package https://github.com/stephens999/ashr N/A RSEM software (version 1.3.1) https://deweylab.github.io/RSEM/ V 1.3.1 STAR RNA-Seq Read Mapper (version 2.7) https://github.com/alexdobin/STAR; https://doi.org/10.1093/ bioinformatics/bts635 V 2.7 FlowJo (version 10.9) TreeStar, Ashland, OR V 10.9 GraphPad (version 10.0.2) https://www.graphpad.com V 10.0.2 Other Bulk cartridge CodePlex Secretome IsoPlexis Cat# CodePlex Inflammation-L Chip 2, CODEPLEX-@L-10-2 All-in-One Fluorescence Microscope Keyence Cat# BZ-X810 CFX96 Touch Real-Time PCR Bio-Rad Cat# CFX96 Touch Real-Time PCR Detection System NovaSeq 6000 Illumina Model: Illumina NovaSeq 6000 BaseSpace Sequence Hub Illumina https://www.illumina.com/products/ by-type/informatics-products/ basespace-sequence-hub.html NovoCyte Quanteon Flow Cytometer Agilent Cat#64-1-1812-1046-4 GentleMACS Octo Dissociator with Heaters Miltenyi Biotech Cat# 130-096-427 NanoDrop One-C NanoDrop Serial #A241601534 Countess 3 Automated Cell Counter Invitrogen Cat #AMQAX2000 Bead Mill Homogenizer 120V (25 mL-5mL) VWR-Avantor Cat#75840-022 DeNovix DS-11 FX Spectrophotometer Qubit https://www.denovix.com/products/ ds-11-fx-spectrophotometer-fluorometer/ 2 mL reinforced Bead Mill tubes VWR-Avantor Cat# 10158-556 0.4 mm glass beads VWR-Avantor Cat# 12621-154 1.4 mm ceramic beads VWR-Avantor Cat# 10158-552 Hard-Shell PCR Plates 96-well, thin wall Bio-Rad Cat# HSP9601 Microseal B seals Bio-Rad Cat# MSB1001 Miltenyi dissociation tubes Miltenyi Biotech Cat# 130-095-927 40mm filters Falcon Cat# 352340 Keyence BZ-X800E Keyence Corporation Cat# BZ-X800E 22 Cell Reports 42, 113294, November 28, 2023 ..

    Article Title: Tumor-mediated microbiota alteration impairs synaptic tagging/capture in the hippocampal CA1 area via IL-1β production.
    Article Snippet: The standard curve and the samples were measured using an BD FACSAriaTM Fusion Flow Cytometers (BD Bioscience, Franklin Lakes, NJ, USA). .. The results were analyzed with the LEGENDplexTM Data Analysis Software Suite from Qognit (https:// legendplex.qognit.com/user/login?next=home), which could differentiate specific beads for each analyte based on their size and fluorescence intensity, where 4000 events had to be acquired per analyte. ..

    Microscopy:

    Article Title: Bordetella spp. block eosinophil recruitment to suppress the generation of early mucosal protection.
    Article Snippet: Cat#130-095-927 MojoSortTM Mouse CD3+ T cell Isolation Kit BioLegend Cat#480024 DynabeadsTM Mouse T-Activator CD3/CD28 T cell Expansion and Activation Beads Gibco Cat #11456D NEBNext Library Quant Kit for Illumina New England Biolabs Cat# E7630L Stranded mRNA Prep Ligation kit Illumina Cat# 20040532 PureLink DNase Set Invitrogen Cat #12185010 Deposited data FASTQ files EMBL-EBI (https://www.ebi. ac.uk/biostudies/arrayexpress/ studies/E-MTAB-13332); LSU Health Sciences Center at Shreveport BioStudies: E-MTAB-13332 Mus musculus reference genome version GRCm39 Genome Reference Consortium (GRC) GenBank: GCA_000001635.9 Mus musculus gene transfer format (.gtf) annotated version GRCm39.105: GCA_000001635.9 NCBI RefSeq RefSeq: GCF_000001635.27-RS_2023_04 Experimental models: Cell lines Murine bone marrow-derived eosinophils Mai et al., 202174 PMID: 33486726 Experimental models: Organisms/strains Mouse: BALB/cJ Jackson Laboratories Cat# 000651; RRID: IMSR_JAX:000651 Mouse: DdblGATA: B6.129S1(C)-Gata1tm6Sho/LvtzJ Jackson Laboratories Cat# 033551; RRID: IMSR_JAX:033551 Mouse: C57BL/6J Jackson Laboratories Cat# 000664; RRID: IMSR_JAX:000664 Mouse: EPX/MBP / : MBP-1 / /EPX / Donation from Dr Jacobsen La Joya PMID: 28515227 Oligonucleotides b-Actin Fw IDT (Integrated DNA Technologies) PMID: 31889098 b-Actin Rv IDT (Integrated DNA Technologies) PMID: 31889098 Il-17 Fw IDT (Integrated DNA Technologies) PMID: 17918201 IL-17 Rv IDT (Integrated DNA Technologies) PMID: 17918201 IFNg Fw IDT (Integrated DNA Technologies) PMID: 23133493 IFNg Rv IDT (Integrated DNA Technologies) PMID: 23133493 CCL-19 F IDT (Integrated DNA Technologies) PMID: 19651862 CCL-19 Rv IDT (Integrated DNA Technologies) PMID: 19651862 (Continued on next page) Cell Reports 42, 113294, November 28, 2023 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER MadCam-1-Fw IDT (Integrated DNA Technologies) PMID: 31526758 MadCam-1-Rv IDT (Integrated DNA Technologies) PMID: 31526758 Software and algorithms LegendPlexTM Data Analysis Software Suite Qognit legendplex.qognit.com Keyence Image Analysis Software (version 1.1.2) Keyence Corporation America Cat# BZ-H4A, BZ-H4M, BZ-H4CM, BZ-H4R qRT-PCR fold-change mRNA expression The Ultimate qPCR Experiment: Producing Publication Quality, Reproducible Data the First Time: Trends in Biotechnology (cell.com) PMID: 30654913 Illumina NovaSeq Control Software v1.7.5; RTA v3 https://support.illumina.com/downloads/ novaseq-control-software-v1-7-5.html V 1.7.5; RTA v3 Trimmomatic adaptor (version 0.38) https://github.com/usadellab/ Trimmomatic/tree/main V 0.38 DESeq2 R package (version 1.34.0) https://doi.org/10.18129/B9.bioc.DESeq2 V 1.34.0 Cluster profiler package (version 4.2.2) https://doi.org/10.18129/ B9.bioc.clusterProfiler V 4.2.2 ashr’ shrunkage package https://github.com/stephens999/ashr N/A RSEM software (version 1.3.1) https://deweylab.github.io/RSEM/ V 1.3.1 STAR RNA-Seq Read Mapper (version 2.7) https://github.com/alexdobin/STAR; https://doi.org/10.1093/ bioinformatics/bts635 V 2.7 FlowJo (version 10.9) TreeStar, Ashland, OR V 10.9 GraphPad (version 10.0.2) https://www.graphpad.com V 10.0.2 Other Bulk cartridge CodePlex Secretome IsoPlexis Cat# CodePlex Inflammation-L Chip 2, CODEPLEX-@L-10-2 All-in-One Fluorescence Microscope Keyence Cat# BZ-X810 CFX96 Touch Real-Time PCR Bio-Rad Cat# CFX96 Touch Real-Time PCR Detection System NovaSeq 6000 Illumina Model: Illumina NovaSeq 6000 BaseSpace Sequence Hub Illumina https://www.illumina.com/products/ by-type/informatics-products/ basespace-sequence-hub.html NovoCyte Quanteon Flow Cytometer Agilent Cat#64-1-1812-1046-4 GentleMACS Octo Dissociator with Heaters Miltenyi Biotech Cat# 130-096-427 NanoDrop One-C NanoDrop Serial #A241601534 Countess 3 Automated Cell Counter Invitrogen Cat #AMQAX2000 Bead Mill Homogenizer 120V (25 mL-5mL) VWR-Avantor Cat#75840-022 DeNovix DS-11 FX Spectrophotometer Qubit https://www.denovix.com/products/ ds-11-fx-spectrophotometer-fluorometer/ 2 mL reinforced Bead Mill tubes VWR-Avantor Cat# 10158-556 0.4 mm glass beads VWR-Avantor Cat# 12621-154 1.4 mm ceramic beads VWR-Avantor Cat# 10158-552 Hard-Shell PCR Plates 96-well, thin wall Bio-Rad Cat# HSP9601 Microseal B seals Bio-Rad Cat# MSB1001 Miltenyi dissociation tubes Miltenyi Biotech Cat# 130-095-927 40mm filters Falcon Cat# 352340 Keyence BZ-X800E Keyence Corporation Cat# BZ-X800E 22 Cell Reports 42, 113294, November 28, 2023 ..

    Sequencing:

    Article Title: Bordetella spp. block eosinophil recruitment to suppress the generation of early mucosal protection.
    Article Snippet: Cat#130-095-927 MojoSortTM Mouse CD3+ T cell Isolation Kit BioLegend Cat#480024 DynabeadsTM Mouse T-Activator CD3/CD28 T cell Expansion and Activation Beads Gibco Cat #11456D NEBNext Library Quant Kit for Illumina New England Biolabs Cat# E7630L Stranded mRNA Prep Ligation kit Illumina Cat# 20040532 PureLink DNase Set Invitrogen Cat #12185010 Deposited data FASTQ files EMBL-EBI (https://www.ebi. ac.uk/biostudies/arrayexpress/ studies/E-MTAB-13332); LSU Health Sciences Center at Shreveport BioStudies: E-MTAB-13332 Mus musculus reference genome version GRCm39 Genome Reference Consortium (GRC) GenBank: GCA_000001635.9 Mus musculus gene transfer format (.gtf) annotated version GRCm39.105: GCA_000001635.9 NCBI RefSeq RefSeq: GCF_000001635.27-RS_2023_04 Experimental models: Cell lines Murine bone marrow-derived eosinophils Mai et al., 202174 PMID: 33486726 Experimental models: Organisms/strains Mouse: BALB/cJ Jackson Laboratories Cat# 000651; RRID: IMSR_JAX:000651 Mouse: DdblGATA: B6.129S1(C)-Gata1tm6Sho/LvtzJ Jackson Laboratories Cat# 033551; RRID: IMSR_JAX:033551 Mouse: C57BL/6J Jackson Laboratories Cat# 000664; RRID: IMSR_JAX:000664 Mouse: EPX/MBP / : MBP-1 / /EPX / Donation from Dr Jacobsen La Joya PMID: 28515227 Oligonucleotides b-Actin Fw IDT (Integrated DNA Technologies) PMID: 31889098 b-Actin Rv IDT (Integrated DNA Technologies) PMID: 31889098 Il-17 Fw IDT (Integrated DNA Technologies) PMID: 17918201 IL-17 Rv IDT (Integrated DNA Technologies) PMID: 17918201 IFNg Fw IDT (Integrated DNA Technologies) PMID: 23133493 IFNg Rv IDT (Integrated DNA Technologies) PMID: 23133493 CCL-19 F IDT (Integrated DNA Technologies) PMID: 19651862 CCL-19 Rv IDT (Integrated DNA Technologies) PMID: 19651862 (Continued on next page) Cell Reports 42, 113294, November 28, 2023 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER MadCam-1-Fw IDT (Integrated DNA Technologies) PMID: 31526758 MadCam-1-Rv IDT (Integrated DNA Technologies) PMID: 31526758 Software and algorithms LegendPlexTM Data Analysis Software Suite Qognit legendplex.qognit.com Keyence Image Analysis Software (version 1.1.2) Keyence Corporation America Cat# BZ-H4A, BZ-H4M, BZ-H4CM, BZ-H4R qRT-PCR fold-change mRNA expression The Ultimate qPCR Experiment: Producing Publication Quality, Reproducible Data the First Time: Trends in Biotechnology (cell.com) PMID: 30654913 Illumina NovaSeq Control Software v1.7.5; RTA v3 https://support.illumina.com/downloads/ novaseq-control-software-v1-7-5.html V 1.7.5; RTA v3 Trimmomatic adaptor (version 0.38) https://github.com/usadellab/ Trimmomatic/tree/main V 0.38 DESeq2 R package (version 1.34.0) https://doi.org/10.18129/B9.bioc.DESeq2 V 1.34.0 Cluster profiler package (version 4.2.2) https://doi.org/10.18129/ B9.bioc.clusterProfiler V 4.2.2 ashr’ shrunkage package https://github.com/stephens999/ashr N/A RSEM software (version 1.3.1) https://deweylab.github.io/RSEM/ V 1.3.1 STAR RNA-Seq Read Mapper (version 2.7) https://github.com/alexdobin/STAR; https://doi.org/10.1093/ bioinformatics/bts635 V 2.7 FlowJo (version 10.9) TreeStar, Ashland, OR V 10.9 GraphPad (version 10.0.2) https://www.graphpad.com V 10.0.2 Other Bulk cartridge CodePlex Secretome IsoPlexis Cat# CodePlex Inflammation-L Chip 2, CODEPLEX-@L-10-2 All-in-One Fluorescence Microscope Keyence Cat# BZ-X810 CFX96 Touch Real-Time PCR Bio-Rad Cat# CFX96 Touch Real-Time PCR Detection System NovaSeq 6000 Illumina Model: Illumina NovaSeq 6000 BaseSpace Sequence Hub Illumina https://www.illumina.com/products/ by-type/informatics-products/ basespace-sequence-hub.html NovoCyte Quanteon Flow Cytometer Agilent Cat#64-1-1812-1046-4 GentleMACS Octo Dissociator with Heaters Miltenyi Biotech Cat# 130-096-427 NanoDrop One-C NanoDrop Serial #A241601534 Countess 3 Automated Cell Counter Invitrogen Cat #AMQAX2000 Bead Mill Homogenizer 120V (25 mL-5mL) VWR-Avantor Cat#75840-022 DeNovix DS-11 FX Spectrophotometer Qubit https://www.denovix.com/products/ ds-11-fx-spectrophotometer-fluorometer/ 2 mL reinforced Bead Mill tubes VWR-Avantor Cat# 10158-556 0.4 mm glass beads VWR-Avantor Cat# 12621-154 1.4 mm ceramic beads VWR-Avantor Cat# 10158-552 Hard-Shell PCR Plates 96-well, thin wall Bio-Rad Cat# HSP9601 Microseal B seals Bio-Rad Cat# MSB1001 Miltenyi dissociation tubes Miltenyi Biotech Cat# 130-095-927 40mm filters Falcon Cat# 352340 Keyence BZ-X800E Keyence Corporation Cat# BZ-X800E 22 Cell Reports 42, 113294, November 28, 2023 ..

    Spectrophotometry:

    Article Title: Bordetella spp. block eosinophil recruitment to suppress the generation of early mucosal protection.
    Article Snippet: Cat#130-095-927 MojoSortTM Mouse CD3+ T cell Isolation Kit BioLegend Cat#480024 DynabeadsTM Mouse T-Activator CD3/CD28 T cell Expansion and Activation Beads Gibco Cat #11456D NEBNext Library Quant Kit for Illumina New England Biolabs Cat# E7630L Stranded mRNA Prep Ligation kit Illumina Cat# 20040532 PureLink DNase Set Invitrogen Cat #12185010 Deposited data FASTQ files EMBL-EBI (https://www.ebi. ac.uk/biostudies/arrayexpress/ studies/E-MTAB-13332); LSU Health Sciences Center at Shreveport BioStudies: E-MTAB-13332 Mus musculus reference genome version GRCm39 Genome Reference Consortium (GRC) GenBank: GCA_000001635.9 Mus musculus gene transfer format (.gtf) annotated version GRCm39.105: GCA_000001635.9 NCBI RefSeq RefSeq: GCF_000001635.27-RS_2023_04 Experimental models: Cell lines Murine bone marrow-derived eosinophils Mai et al., 202174 PMID: 33486726 Experimental models: Organisms/strains Mouse: BALB/cJ Jackson Laboratories Cat# 000651; RRID: IMSR_JAX:000651 Mouse: DdblGATA: B6.129S1(C)-Gata1tm6Sho/LvtzJ Jackson Laboratories Cat# 033551; RRID: IMSR_JAX:033551 Mouse: C57BL/6J Jackson Laboratories Cat# 000664; RRID: IMSR_JAX:000664 Mouse: EPX/MBP / : MBP-1 / /EPX / Donation from Dr Jacobsen La Joya PMID: 28515227 Oligonucleotides b-Actin Fw IDT (Integrated DNA Technologies) PMID: 31889098 b-Actin Rv IDT (Integrated DNA Technologies) PMID: 31889098 Il-17 Fw IDT (Integrated DNA Technologies) PMID: 17918201 IL-17 Rv IDT (Integrated DNA Technologies) PMID: 17918201 IFNg Fw IDT (Integrated DNA Technologies) PMID: 23133493 IFNg Rv IDT (Integrated DNA Technologies) PMID: 23133493 CCL-19 F IDT (Integrated DNA Technologies) PMID: 19651862 CCL-19 Rv IDT (Integrated DNA Technologies) PMID: 19651862 (Continued on next page) Cell Reports 42, 113294, November 28, 2023 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER MadCam-1-Fw IDT (Integrated DNA Technologies) PMID: 31526758 MadCam-1-Rv IDT (Integrated DNA Technologies) PMID: 31526758 Software and algorithms LegendPlexTM Data Analysis Software Suite Qognit legendplex.qognit.com Keyence Image Analysis Software (version 1.1.2) Keyence Corporation America Cat# BZ-H4A, BZ-H4M, BZ-H4CM, BZ-H4R qRT-PCR fold-change mRNA expression The Ultimate qPCR Experiment: Producing Publication Quality, Reproducible Data the First Time: Trends in Biotechnology (cell.com) PMID: 30654913 Illumina NovaSeq Control Software v1.7.5; RTA v3 https://support.illumina.com/downloads/ novaseq-control-software-v1-7-5.html V 1.7.5; RTA v3 Trimmomatic adaptor (version 0.38) https://github.com/usadellab/ Trimmomatic/tree/main V 0.38 DESeq2 R package (version 1.34.0) https://doi.org/10.18129/B9.bioc.DESeq2 V 1.34.0 Cluster profiler package (version 4.2.2) https://doi.org/10.18129/ B9.bioc.clusterProfiler V 4.2.2 ashr’ shrunkage package https://github.com/stephens999/ashr N/A RSEM software (version 1.3.1) https://deweylab.github.io/RSEM/ V 1.3.1 STAR RNA-Seq Read Mapper (version 2.7) https://github.com/alexdobin/STAR; https://doi.org/10.1093/ bioinformatics/bts635 V 2.7 FlowJo (version 10.9) TreeStar, Ashland, OR V 10.9 GraphPad (version 10.0.2) https://www.graphpad.com V 10.0.2 Other Bulk cartridge CodePlex Secretome IsoPlexis Cat# CodePlex Inflammation-L Chip 2, CODEPLEX-@L-10-2 All-in-One Fluorescence Microscope Keyence Cat# BZ-X810 CFX96 Touch Real-Time PCR Bio-Rad Cat# CFX96 Touch Real-Time PCR Detection System NovaSeq 6000 Illumina Model: Illumina NovaSeq 6000 BaseSpace Sequence Hub Illumina https://www.illumina.com/products/ by-type/informatics-products/ basespace-sequence-hub.html NovoCyte Quanteon Flow Cytometer Agilent Cat#64-1-1812-1046-4 GentleMACS Octo Dissociator with Heaters Miltenyi Biotech Cat# 130-096-427 NanoDrop One-C NanoDrop Serial #A241601534 Countess 3 Automated Cell Counter Invitrogen Cat #AMQAX2000 Bead Mill Homogenizer 120V (25 mL-5mL) VWR-Avantor Cat#75840-022 DeNovix DS-11 FX Spectrophotometer Qubit https://www.denovix.com/products/ ds-11-fx-spectrophotometer-fluorometer/ 2 mL reinforced Bead Mill tubes VWR-Avantor Cat# 10158-556 0.4 mm glass beads VWR-Avantor Cat# 12621-154 1.4 mm ceramic beads VWR-Avantor Cat# 10158-552 Hard-Shell PCR Plates 96-well, thin wall Bio-Rad Cat# HSP9601 Microseal B seals Bio-Rad Cat# MSB1001 Miltenyi dissociation tubes Miltenyi Biotech Cat# 130-095-927 40mm filters Falcon Cat# 352340 Keyence BZ-X800E Keyence Corporation Cat# BZ-X800E 22 Cell Reports 42, 113294, November 28, 2023 ..

    Polymerase Chain Reaction:

    Article Title: Bordetella spp. block eosinophil recruitment to suppress the generation of early mucosal protection.
    Article Snippet: Cat#130-095-927 MojoSortTM Mouse CD3+ T cell Isolation Kit BioLegend Cat#480024 DynabeadsTM Mouse T-Activator CD3/CD28 T cell Expansion and Activation Beads Gibco Cat #11456D NEBNext Library Quant Kit for Illumina New England Biolabs Cat# E7630L Stranded mRNA Prep Ligation kit Illumina Cat# 20040532 PureLink DNase Set Invitrogen Cat #12185010 Deposited data FASTQ files EMBL-EBI (https://www.ebi. ac.uk/biostudies/arrayexpress/ studies/E-MTAB-13332); LSU Health Sciences Center at Shreveport BioStudies: E-MTAB-13332 Mus musculus reference genome version GRCm39 Genome Reference Consortium (GRC) GenBank: GCA_000001635.9 Mus musculus gene transfer format (.gtf) annotated version GRCm39.105: GCA_000001635.9 NCBI RefSeq RefSeq: GCF_000001635.27-RS_2023_04 Experimental models: Cell lines Murine bone marrow-derived eosinophils Mai et al., 202174 PMID: 33486726 Experimental models: Organisms/strains Mouse: BALB/cJ Jackson Laboratories Cat# 000651; RRID: IMSR_JAX:000651 Mouse: DdblGATA: B6.129S1(C)-Gata1tm6Sho/LvtzJ Jackson Laboratories Cat# 033551; RRID: IMSR_JAX:033551 Mouse: C57BL/6J Jackson Laboratories Cat# 000664; RRID: IMSR_JAX:000664 Mouse: EPX/MBP / : MBP-1 / /EPX / Donation from Dr Jacobsen La Joya PMID: 28515227 Oligonucleotides b-Actin Fw IDT (Integrated DNA Technologies) PMID: 31889098 b-Actin Rv IDT (Integrated DNA Technologies) PMID: 31889098 Il-17 Fw IDT (Integrated DNA Technologies) PMID: 17918201 IL-17 Rv IDT (Integrated DNA Technologies) PMID: 17918201 IFNg Fw IDT (Integrated DNA Technologies) PMID: 23133493 IFNg Rv IDT (Integrated DNA Technologies) PMID: 23133493 CCL-19 F IDT (Integrated DNA Technologies) PMID: 19651862 CCL-19 Rv IDT (Integrated DNA Technologies) PMID: 19651862 (Continued on next page) Cell Reports 42, 113294, November 28, 2023 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER MadCam-1-Fw IDT (Integrated DNA Technologies) PMID: 31526758 MadCam-1-Rv IDT (Integrated DNA Technologies) PMID: 31526758 Software and algorithms LegendPlexTM Data Analysis Software Suite Qognit legendplex.qognit.com Keyence Image Analysis Software (version 1.1.2) Keyence Corporation America Cat# BZ-H4A, BZ-H4M, BZ-H4CM, BZ-H4R qRT-PCR fold-change mRNA expression The Ultimate qPCR Experiment: Producing Publication Quality, Reproducible Data the First Time: Trends in Biotechnology (cell.com) PMID: 30654913 Illumina NovaSeq Control Software v1.7.5; RTA v3 https://support.illumina.com/downloads/ novaseq-control-software-v1-7-5.html V 1.7.5; RTA v3 Trimmomatic adaptor (version 0.38) https://github.com/usadellab/ Trimmomatic/tree/main V 0.38 DESeq2 R package (version 1.34.0) https://doi.org/10.18129/B9.bioc.DESeq2 V 1.34.0 Cluster profiler package (version 4.2.2) https://doi.org/10.18129/ B9.bioc.clusterProfiler V 4.2.2 ashr’ shrunkage package https://github.com/stephens999/ashr N/A RSEM software (version 1.3.1) https://deweylab.github.io/RSEM/ V 1.3.1 STAR RNA-Seq Read Mapper (version 2.7) https://github.com/alexdobin/STAR; https://doi.org/10.1093/ bioinformatics/bts635 V 2.7 FlowJo (version 10.9) TreeStar, Ashland, OR V 10.9 GraphPad (version 10.0.2) https://www.graphpad.com V 10.0.2 Other Bulk cartridge CodePlex Secretome IsoPlexis Cat# CodePlex Inflammation-L Chip 2, CODEPLEX-@L-10-2 All-in-One Fluorescence Microscope Keyence Cat# BZ-X810 CFX96 Touch Real-Time PCR Bio-Rad Cat# CFX96 Touch Real-Time PCR Detection System NovaSeq 6000 Illumina Model: Illumina NovaSeq 6000 BaseSpace Sequence Hub Illumina https://www.illumina.com/products/ by-type/informatics-products/ basespace-sequence-hub.html NovoCyte Quanteon Flow Cytometer Agilent Cat#64-1-1812-1046-4 GentleMACS Octo Dissociator with Heaters Miltenyi Biotech Cat# 130-096-427 NanoDrop One-C NanoDrop Serial #A241601534 Countess 3 Automated Cell Counter Invitrogen Cat #AMQAX2000 Bead Mill Homogenizer 120V (25 mL-5mL) VWR-Avantor Cat#75840-022 DeNovix DS-11 FX Spectrophotometer Qubit https://www.denovix.com/products/ ds-11-fx-spectrophotometer-fluorometer/ 2 mL reinforced Bead Mill tubes VWR-Avantor Cat# 10158-556 0.4 mm glass beads VWR-Avantor Cat# 12621-154 1.4 mm ceramic beads VWR-Avantor Cat# 10158-552 Hard-Shell PCR Plates 96-well, thin wall Bio-Rad Cat# HSP9601 Microseal B seals Bio-Rad Cat# MSB1001 Miltenyi dissociation tubes Miltenyi Biotech Cat# 130-095-927 40mm filters Falcon Cat# 352340 Keyence BZ-X800E Keyence Corporation Cat# BZ-X800E 22 Cell Reports 42, 113294, November 28, 2023 ..



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